As the title suggests I have animations nested within 2 and 3 compositions deep in my project which all play within their own compositions (I have however experienced a few issues where some of the puppet tool animations would jump to a position I haven't told them to on playback), but when I come back out to the main composition there is no movement at all.

Also when I animate from the main composition I'm getting some strange masking issues, however I haven't added any masking (Reference image attached).

I have also had similar problems with masks not appearing where they should and video footage appearing in my composition that has not been imported into my AE project, or even exists on my local hard drive.

I tried resetting AE preferences and uninstalling and reinstalling, nothing worked except starting a new project.

Looks like you have collapse transformations enabled on something animated with the puppet tool. These two features can conflict with each other. Try turning off collapse transforms and see what happens.

That seems to have solved the problem in this instance. However after many years using After Effects in this way it's the first time I've encountered this issue. Do you know if it'll be resolved moving forward?

this issue is a result of the render order pipeline which was always there in Ae and probably will be forever. puppet is an effect and effects are applied before transformations, unless you click the collapse switch and it reverses the order. therefore you should not change or animate transformations for a collapsed layer or precomp when using the puppet effect. this is from the help files:

Don’t animate the position or scale of a continuously rasterized layer with layer transformations if you are also animating the layer with the Puppet tools. The render order for continuously rasterized layers—such as shape layers and text layers—is different from the render order for raster layers. You can precompose the shape layer and use the Puppet tools on the precomposition layer, or you can use the Puppet tools to transform the shapes within the layer. (See Render order and collapsing transformations and Continuously rasterize a layer containing vector graphics.)

I've even re-created the same animation in the previous version and had no issues.

maybe it's not the same issue. if you really want to get to the bottom of this then isolate your problem. one Comp, maybe one layer - try and see when and how exactly it breaks. then compare to old version. if you are experiencing inconsistency between how it breaks between versions then report it here. if this is a bug we could report it and make Ae better for all of us. feel free to update this thread, I am personally interested in anything that breaks after effects or only seem to break it.

I collapsed transformations and enabled back again. it did half the job. There were problems with some rotations. I activated: On Transparent (check first, in some animations work and others it doesn't.) Everything seems fine now.

activated: On Transparent (check first, in some animations work and others it doesn't.)

on transparent makes sure that no pixels outside the mesh will be shown. this could look as if it solved your problem in some cases but as the help files explain - working with collapse+puppet+animation transformation on is really making a mess and results can be unpredictable.